For three weeks, the commander of the Third Air Force combed through thousands of pages of court testimony, scrutinized cellphone records and photographs, considered nearly 100 letters for clemency and twice watched the 3½-hour interrogation of a colonel-select convicted of sexually assaulting a houseguest.

The case of Lt. Col. James Wilkerson, an F-16 pilot and former inspector general at Aviano Air Base, Italy, bothered the commander from the beginning. As the court-martial convening authority, Lt. Gen. Craig Franklin struggled over the decision to send Wilkerson to trial in the first place. There was no physical evidence and no confession — just the word of the accuser against that of the accused and his wife.

The guilty verdict handed down Nov. 2 by a panel of officers Franklin selected surprised the general. After the intensive three-week review, Franklin concluded there was not enough evidence to support the conviction. Against the recommendation of his staff judge advocate, Franklin overturned the guilty verdict, freeing Wilkerson from a military prison and restoring him to the Air Force.

Any other action “would have been an act of cowardice on my part and a breach of my integrity,” Franklin wrote in a March 12 memo to Air Force Secretary Michael Donley.

The six-page document released April 10 provided the first insight into the three-star’s Feb. 26 decision, which unleashed a conflagration of criticism on Capitol Hill and led to a Defense Department proposal to strip commanders of the power to override convictions.

Franklin has remained silent on the Wilkerson case, at least publicly. In the letter to Donley, Franklin wrote he was under no obligation to explain his actions but was making a one-time exception “due to the ongoing controversy … in the ‘court of public opinion.’”

Franklin wrote that the accuser, 49-year-old American civilian Kimberly Hanks, gave shaky and inconsistent accounts of the events of the night in question and could not remember key details: She could not identify the bed in which she said she was assaulted, she did not know whether Wilkerson had facial hair and she couldn’t have left the house the way she claimed.

Wilkerson’s wife “was substantially consistent” and Wilkerson maintained his innocence throughout a 3½-hour interview with investigators who “utilized the full gamut of … techniques in attempts to garner incriminating statements,” Franklin wrote.

Further, at least one of the 91 clemency letters on Wilkerson’s behalf came from a friend of Hanks, Franklin said. The woman suggested Hanks might have lied about what happened because her civilian contract at Aviano was coming up for renewal and an alcohol-related incident could jeopardize it.

Hanks had been drinking the night she and a group of Air Force officers and noncommissioned officers showed up at the Wilkerson house after attending a concert and club, according to trial testimony. All of the guests eventually left, except for Hanks. Beth Wilkerson offered the woman a guest bedroom.

Hanks alleged she awoke in the middle of the night to find Wilkerson in her bed, his hand down her pants, and Beth Wilkerson at the door shouting at Hanks to leave. Beth Wilkerson said her husband stayed in his own bed; after finding Hanks walking noisily around their home, she told the woman to go to bed or leave. Hanks left, Beth Wilkerson said.

Franklin listed 18 reasons that he said raised reasonable doubt of Wilkerson’s guilt. He also wrote that while his staff judge advocate recommended the conviction stand, he “fully respected my decision to disapprove the findings in this court case.”

The victim’s story was not impossible, Franklin said, and there was some evidence he could not reconcile.

“The majority of these inconsistencies had plausible alternate explanations,” the commander wrote.

He called the clemency package the most extensive he had ever seen.

“I was perplexed in relation to this conundrum — Lt. Col. Wilkerson was a selectee for promotion to full colonel, a wing inspector general, a career officer, and described as a doting father and husband. However, according to … the prosecution, [Wilkerson], in the middle of the night, decided to leave his wife sleeping in bed, walk downstairs past the room of his only son … and then decided to commit the egregious crime of sexually assaulting a sleeping woman who he and his wife had only met earlier that night,” Franklin said.

The release of the letter and hundreds of pages of other documents from the case did little to appease lawmakers and victim advocates who, in the aftermath of Franklin’s decision, demanded answers from top military officials and called for changes to the Uniform Code of Military Justice. One of those documents, a letter from Wilkerson to Franklin appealing for clemency, indicated the two had once flown together.

“You may not recall this sir, but you and I actually flew together, once in Iraq. You were ‘Red Tail 1’ at the time, and I was the director of operations for the 77th Fighter Squadron ‘Gamblers,’” Wilkerson wrote in his appeal for clemency.

The commander’s reliance, at least to some degree, on the clemency letters that included information ruled inadmissible at court-martial, underscore the flaws of the military justice system, Nancy Parrish, president of Protect Our Defenders, said in a statement.

“Rather than rely on the credible determinations of the senior members of the jury he selected, Franklin chose to accept the word of Wilkerson’s supporters,” Parrish said.

“What Gen. Franklin is saying, with great audacity, is he knows better … that a campaign by a convicted criminal with clemency letters can trump a court proceeding,” Speier said.

March 23-24, 2012

The accuser, Kimberly Hanks, a 49-year-old American civilian, attends a concert and visits a club at Aviano Air Base, Italy, with a group of Air Force officers and noncommissioned officers. Afterward, they go to the home of Lt. Col. James Wilkerson. Hanks accepts an invitation to stay the night in a guest room. The other guests leave.

April 19, 2012

In an interview with the Air Force Office of Special Investigations, Hanks says she awoke to find Wilkerson in her bed, touching her sexually, and then Wilkerson’s wife, Beth, kicked her out of the house. The Wilkersons claim Wilkerson never left his own room and that Hanks left voluntarily when Beth Wilkerson told her to go to bed or leave.

May 2012

Brig. Gen. Scott Zobrist, commander of the 31st Fighter Wing at Aviano, removes Wilkerson from his job as inspector general, pending outcome of the OSI investigation.

June 26, 2012

Investigating officer recommends Wilkerson face court-martial on charges of abusive sexual contact, aggravated sexual assault and conduct unbecoming an officer and gentleman. “In the end, what compels my recommendation … is the absence of any apparent motive on the part of Ms. Hanks to fabricate the allegations,” the investigator wrote.

Nov. 2, 2012

A jury of four colonels and one lieutenant colonel convict Wilkerson on all charges. The all-male panel sentences him to one year in prison and dismissal from the Air Force, stripping Wilkerson of his retirement and benefits.

January 14, 2013

Wilkerson, who had been selected for promotion to colonel prior to the allegations, is removed from the promotions list.

Feb. 26, 2013

Lt. Gen. Craig Franklin, Third Air Force commander, uses his power as the convening authority to overturn Wilkerson’s conviction. The decision, which is agains+t the recommendation of Franklin’s staff judge advocate, is the equivalent of an acquittal. The same day, Wilkerson is released from a Charleston, S.C., brig.

March 5, 2013

Sen. Claire McCaskill, D-Mo, is among the first of many lawmakers to lambast Franklin’s decision and calls for changes to the Uniform Code of Military Justice.

March 12, 2013

Reps. Jackie Speier, D-Calif., Bruce Braley, D-Iowa, and Patrick Meehan, R-Penn., introduce the Military Judicial Reform Act that would remove from a commander the authority to overturn convictions and reduce sentences.

March 13, 2013

McCaskill announces she is drafting a bill in the Senate that would strip commanders of the power to overturn convictions and require them to provide a written explanation when reducing sentences.

March 29, 2013

The Air Force says Wilkerson has returned to active duty as the 12th Air Force’s chief of flight safety at Davis-Monthan Air Force Base, Ariz.

April 8, 2013

Defense Secretary Chuck Hagel proposes changes to the UCMJ similar to McCaskill’s proposal: Remove from the convening authority the power to alter verdicts for major offenses and require documentation for reducing sentences.

April 10, 2013

The Air Force makes public a six-page letter to Air Force Secretary Michael Donley from Franklin, who defends his decision to dismiss Wilkerson’s conviction.